3. How can I determine how a clone relates to the assembly if there is no insert sequence?

Clone information is contained in the NCBI Clone Registry
http://www.ncbi.nlm.nih.gov/genome/clone/

You can find Clone information in the Map Viewer.
    Maps with may contain clone information:   Clone, BES_clone, Genbank_DNA, FISH_Clone, Component

Mouse only (for now):
CloneFinder: http://www.ncbi.nlm.nih.gov/genome/clone/clonefinder/CloneFinder.html